We have been looking for a simple and fast way of #genotyping a #bam file at known sites that we get from a reference #vcf.

We ended up using #freebayes with -@ -l --report-monomorphic options.

BUT I was quite surprised by the lack of information and clear documentation for performing this seemingly trivial task without going through the whole SNP calling stuff (we don't want to do it).

Did we miss something ? Is there a standard, well documented method out there ?